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7.6 years ago
kanwarjag
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1.2k
A question about browser based TCGA expression data (https://tools.stamlab.org/tcga/?gene=MYB) . It is a follow up question previously discussed @ C: One gene association with cancer types 1. It takes level 3 TCGA data or some other level. 2. The figure shows TPM, I was wondering how the RNA seq data has been finally analyzed in the backend. Is it RSEM or RPKM level analysis 3. Raw CSV will output raw read count data or it has been preprocessed in some way.
It appears to utilize level 2 data, since they link to a page explaining about it. Hard to say what they are doing in their backend, have you tried contacting the tool developers?